3-Isopropylmalate (YMDB00368)

Identification

YMDB ID

YMDB00368

Name

3-Isopropylmalate

Species

Saccharomyces cerevisiae

Strain

Baker's yeast

Description

3-Isopropylmalic acid, also known as 3-isopropylmalate, belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group. Based on a literature review a small amount of articles have been published on 3-Isopropylmalic acid.

Structure

MOL SDF PDB SMILES InChI

Synonyms

(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioate
(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid
(2R,3S)-2-hydroxy-3-isopropylsuccinate
(2R,3S)-2-hydroxy-3-isopropylsuccinic acid
(2R,3S)-3-carboxy-2-hydroxy-4-methylpentanoate
(2R,3S)-3-carboxy-2-hydroxy-4-methylpentanoic acid
(2R,3S)-3-Isopropylmalate
(2R,3S)-3-isopropylmalic acid
2-D-threo-Hydroxy-3-carboxy-isocaproate
2-D-threo-Hydroxy-3-carboxy-isocaproic acid
2-D-threo-hydroxy-3-carboxyisocaproate
2-D-threo-hydroxy-3-carboxyisocaproic acid
3-3-isopropylmalic acid
3-Carboxy-2-hydroxy-4-methylpentanoate
3-Carboxy-2-hydroxy-4-methylpentanoic acid
3-Isopropylmalate
IPM
3-Isopropylmalic acid
beta-Isopropylmalate, erythro-(L)-isomer
beta-Isopropylmalate
(2R,3S)-2-Hydroxy-3-(1-methylethyl)butanedioic acid
2-Hydroxy-3-(1-methylethyl)butanedioic acid
Isopropylmalate
Isopropylmalic acid
beta-Isopropylmalic acid
β-Isopropylmalic acid

CAS number

921-28-8

Weight

Average: 176.1672
Monoisotopic: 176.068473494

InChI Key

RNQHMTFBUSSBJQ-CRCLSJGQSA-N

InChI

InChI=1S/C7H12O5/c1-3(2)4(6(9)10)5(8)7(11)12/h3-5,8H,1-2H3,(H,9,10)(H,11,12)/t4-,5+/m0/s1

IUPAC Name

(2R,3S)-2-hydroxy-3-(propan-2-yl)butanedioic acid

Traditional IUPAC Name

(2R,3S)-3-isopropylmalic acid

Chemical Formula

C₇H₁₂O₅

SMILES

[H]OC(=O)[C@]([H])(O[H])[C@@]([H])(C(=O)O[H])C([H])(C([H])([H])[H])C([H])([H])[H]

Chemical Taxonomy

Description

belongs to the class of organic compounds known as hydroxy fatty acids. These are fatty acids in which the chain bears a hydroxyl group.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Hydroxy fatty acids

Alternative Parents

Substituents

Beta-hydroxy acid
Branched fatty acid
Hydroxy fatty acid
Short-chain hydroxy acid
Methyl-branched fatty acid
Alpha-hydroxy acid
Hydroxy acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Carbonyl group
Alcohol
Hydrocarbon derivative
Organic oxide
Organic oxygen compound
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

3-isopropylmalic acid (CHEBI:43468 )

Physical Properties

State

Solid

Charge

Melting point

Not Available

Experimental Properties

Property	Value	Reference
Water Solubility	Not Available	PhysProp
LogP	Not Available	PhysProp

Predicted Properties

Property	Value	Source
Water Solubility	83.3 g/L	ALOGPS
logP	0.28	ALOGPS
logP	0.16	ChemAxon
logS	-0.33	ALOGPS
pKa (Strongest Acidic)	3.68	ChemAxon
pKa (Strongest Basic)	-4	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	94.83 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	38.6 m³·mol⁻¹	ChemAxon
Polarizability	16.47 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	1	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	Yes	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Biological Properties

Cellular Locations

cytoplasm

Organoleptic Properties

Not Available

SMPDB Pathways

Leucine Biosynthesis

PW002475

KEGG Pathways

Valine, leucine and isoleucine biosynthesis

ec00290

SMPDB Reactions

2-Isopropylmaleic acid + water → 3-Isopropylmalate

3-Isopropylmalate + NAD → NADH + hydron + (2S)-2-Isopropyl-3-oxosuccinate

KEGG Reactions

3-Isopropylmalate + S-Adenosylmethionine → S-Adenosylhomocysteine + 3-hydroxy-2-isopropyl-4-methoxy-4-oxobutanoate

3-Isopropylmalate ↔ water + 2-Isopropylmaleic acid

NAD + 3-Isopropylmalate → NADH + (2S)-2-Isopropyl-3-oxosuccinate + hydron

Concentrations

Intracellular Concentrations

Not Available

Extracellular Concentrations

Not Available

Spectra

Spectrum Type	Description	Splash Key	View
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	JSpectraViewer \| MoNA
GC-MS	GC-MS Spectrum - GC-EI-TOF (Non-derivatized)	splash10-0002-0920000000-4ec856cc4eb69ab95ccc	JSpectraViewer \| MoNA
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0006-9400000000-a5c729805d94db1fb7b3	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (3 TMS) - 70eV, Positive	splash10-00bl-9135000000-1982df651c1931669dae	JSpectraViewer
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0a7i-1900000000-224a91a676e183e74333	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-06sl-7900000000-b06817c1e6edcae6d425	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052o-9300000000-479bb2145817abc0bf1a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-0059-1900000000-acde792ba60cae65a216	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-0far-9700000000-cf8f9dd2b32cfd503f42	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0a59-9100000000-138111afc561c6d0a2ec	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-03ei-3900000000-99922dc6120c0bc9d5ac	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-9300000000-6c8d0a906ce3776c4769	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052f-9000000000-229b51add43b0209aa10	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-001i-1900000000-bcc925b37cd5d5f31b5a	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-01q0-7900000000-222a48c445cf7526d6e6	JSpectraViewer
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-0019-9100000000-6003ddbcaf34c522b89a	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer
1D NMR	1H NMR Spectrum	Not Available	JSpectraViewer
1D NMR	13C NMR Spectrum	Not Available	JSpectraViewer

References

References:

UniProt Consortium (2011). "Ongoing and future developments at the Universal Protein Resource." Nucleic Acids Res 39:D214-D219.21051339
Herrgard, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Bluthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novere, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasic, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kirdar, B., Penttila, M., Klipp, E., Palsson, B. O., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J., Kell, D. B. (2008). "A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology." Nat Biotechnol 26:1155-1160.18846089
Katz, J. E., Dumlao, D. S., Wasserman, J. I., Lansdown, M. G., Jung, M. E., Faull, K. F., Clarke, S. (2004). "3-Isopropylmalate is the major endogenous substrate of the Saccharomyces cerevisiae trans-aconitate methyltransferase." Biochemistry 43:5976-5986.15147181

Synthesis Reference:

Not Available

External Links:

Resource	Link
CHEBI ID	43468
HMDB ID	HMDB12156
Pubchem Compound ID	5462261
Kegg ID	C04411
ChemSpider ID	4575349
FOODB ID	FDB028813
Wikipedia ID	Isopropylmalic acid
BioCyc ID	2-D-THREO-HYDROXY-3-CARBOXY-ISOCAPROATE

Enzymes

Protein Details

1. 3-isopropylmalate dehydratase

General function:: Involved in 3-isopropylmalate dehydratase activity
Specific function:: Catalyzes the isomerization between 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate
Gene Name:: LEU1
Uniprot ID:: P07264
Molecular weight:: 85793.70313

Reactions

(2R,3S)-3-isopropylmalate → (2S)-2-isopropylmaleate + H(2)O.
(2S)-2-isopropylmaleate + H(2)O → (2S)-2-isopropylmalate.

Protein Details

2. 3-isopropylmalate dehydrogenase

General function:: Involved in magnesium ion binding
Specific function:: Catalyzes the oxidation of 3-carboxy-2-hydroxy-4- methylpentanoate (3-isopropylmalate) to 3-carboxy-4-methyl-2- oxopentanoate. The product decarboxylates to 4-methyl-2 oxopentanoate
Gene Name:: LEU2
Uniprot ID:: P04173
Molecular weight:: 38952.5

Reactions

(2R,3S)-3-isopropylmalate + NAD(+) → 4-methyl-2-oxopentanoate + CO(2) + NADH.

Protein Details

3. Trans-aconitate 3-methyltransferase

General function:: Involved in methyltransferase activity
Specific function:: Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate and 3-isopropylmalate at high affinity and of other molecules like cis-aconitate, isocitrate, and citrate at lower velocities and affinities. The function of trans-aconitate methylation appears to be in reducing the toxicity of this spontaneous breakdown product of cis-aconitate. The role of 3-isopropylmalate methylation is unclear but may represent a metabolic branch at 3-isopropylmalate, where some of the material is taken in the pathway leading to leucine and some is taken in a pathway to the 3-isopropylmalate methyl ester, a molecule that provides a signal to switch from vegetative to invasive growth in response to amino acid starvation
Gene Name:: TMT1
Uniprot ID:: P32643
Molecular weight:: 34768.0

Reactions

S-adenosyl-L-methionine + trans-aconitate → S-adenosyl-L-homocysteine + (E)-2-(methoxycarbonylmethyl)butenedioate.

Structure for #<Compound:0xadba5f24>

Enzymes

Reactions

Reactions

Reactions